Determination of H-Atom Positions in Organic Crystal Structures by NEXAFS Combined with Density Functional Theory: a Study of Two-Component Systems Containing Isonicotinamide

It is important to be able to identify the precise position of H-atoms in hydrogen bonding interactions to fully understand the effects on the structure and properties of organic crystals. Using a combination of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory (DFT) quantum chemistry calculations, we demonstrate the sensitivity of core-level X-ray spectroscopy to the precise H-atom position within a donor-proton-acceptor system. Exploiting this sensitivity, we then combine the predictive power of DFT with the experimental NEXAFS, confirming the H-atom position identified using single-crystal X-ray diffraction (XRD) techniques more easily than using other H-atom sensitive techniques, such as neutron diffraction. This proof of principle experiment confirms the H-atom positions in structures obtained from XRD, providing evidence for the potential use of NEXAFS as a more accurate and easier method of locating H-atoms within organic crystals.


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The three two-component organic crystals studied in this work are: isonicotinamide 2,4-dinitrobenzoic acid (C 13 H 10 N 4 O 7 ), isonicotinamide 3,5-diniotrobenzoic acid (C 13 H 10 N 4 O 7 ) and isonicotinamide phthalic acid (C 20 H 18 N 2 O 6 ). The chemical structures are shown in Figure S1 including all of the relevant intermolecular hydrogen bonding and proton transfer interactions. These interactions have previously been characterized using X-ray diffraction (XRD), and the bond distance and angle parameters for each interaction are shown in Table S1. 1 NEXAFS normalization procedure for NAP-NEXAFS using the gas phase (with longer path length) as the background I 0 Due to the difficulties of measuring the background signal when using NAP-NEXAFS, measurements of the He gas phase (the chamber with sample removed from the beam path) were taken to provide a background. Significant features are present in this spectrum at the nitrogen K-edge due to the use of a silicon nitride membrane in the beamline.
The absorption coefficient (intensity of a NEXAFS spectrum) is defined by µ, where I is the measured spectrum and I 0 is the background spectrum: = 0 By using NAP-NEXAFS, the measurement of the I 0 background becomes non-trivial, with the effect of the gas phase important in the normalization of the measured spectra. To measure an approximate I 0 , a gas phase measurement (by removing the sample plate from the beam path) was taken at each of the required absorption edges. Because of the difference in path length through the gas phase compared

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to the measurements of samples, this approximate I 0 is offset by a value n and scaled by a factor m, resulting in I 0 * . * 0 = 0 + Through a series of rearrangements, we can then obtain the true absorption spectrum, divided by a constant m, which is dependent upon a single variable n, which is fit to best model the spectrum baseline.
The value of n should be a spectrometer and condition dependent constant, and results in the standard equation where the value is 0 (i.e. no offset). Therefore, to identify the appropriate value of n, we suggest minimizing the value off n while retaining a baseline with physical meaning (i.e. no negative obtrusions). We found a value of n=0.005 appropriate for our experiments.

Fitted spectra -peak parameters
Fitting parameters have been determined using the Athena XAS analysis software 2 to fit Gaussian peaks to the NEXAFS spectra. These fits, shown in Table S2 are consistent with our previous XPS study 3 and the relative intensities align well with the calculated DFT spectra. in the experimental spectrum, as seen in Figure S2. This amide nitrogen is highly affected by the longer range interactions, and in these cases the DFT calculation overestimates the relaxation effect of the additional interactions in the system leading to the shift indicated by the arrows in Figure S2.

Crystal component spectra
The Individual components of the three crystals were also measured to determine the difference spectra between the sum of the components and the formed crystal. These are shown in Figure S3.
Isonicotinamide has three clear peaks corresponding to the transitions from the core level N 1s orbitals to the 1π*, 2π* and 3π* orbitals respectively. In pure isonicotinamide, the core level of both the pyridine ring and amide nitrogen are at the same energy (as observed in XPS measurement) and therefore both contribute to each peak.

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The spectra of 35DNBA and 24DNBA are very similar, with slightly different σ* resonances. The spectrum of 24DNBA also has an additional feature at 400 eV, although this is anticipated to be some form of contamination, as there should not be a feature at this energy. Importantly, this small peak does not appear to affect the difference spectra as seen in the manuscript.

Density Functional Theory Calculation Details
Example input files and the xyz files for the calculations are included here for reference purposes.
*.xyz files were obtained from the CSD based on XRD structure refinement. Most TDDFT calculations were done directly using these structures, but some were also carried out after an optimization calculation of the hydrogens in the structure.

Effect of Basis set and Exchange Correlation functional on the calculated NEXAFS spectra
As mentioned in the main manuscript, to ensure an appropriate basis set and exchange correlation functional were utilized in the calculations, a series of tests were completed to ensure the basis set convergence was reasonable (at least in the region of the spectrum of interest) and the exchange correlation functional gave reasonable results. Figure S4 shows the calculated NEXAFS spectrum of IN35DNBA using three different basis sets. The standard triple zeta valence polarized, with additional polarization functions, and augmented with additional basis functions. The important feature to note is that the basis set does not affect the position or intensity of the main N 1s → π* transitions.
The two exchange correlation functionals tested were B3LYP and SRC1 (Utilizing the error function based range separation method mixing BLYP and Hartree Fock exchange components). These calculations were done on the "crystal structure" from the database, so no geometry optimization was required, and therefore it is the NEXAFS spectrum calculation (TDDFT) that we are probing. Figure   S5 shows the effect of the two functionals, with B3LYP reproducing a spectrum resembling S9 experimental data, while SRC1 does not require any photon energy scale calibration. However, the relative peak positions are off compared to experiment and therefore the B3LYP functional was used.

Effect of Exchange Correlation Functional on Geometry Optimization
For completeness, we also include here the test of the two exchange correlation functionals for geometry optimization. Having optimized the geometry using the two separate functionals, Figure S6 shows the Calculated NEXAFS spectra, using the B3LYP functional for the TDDFT calculation as decided previously. Both exchange correlation functionals result in almost indistinguishable NEXAFS spectra, with only a few very minor differences in peak intensity between the two optimized structures.
Therefore, since the choice of functional for geometry optimization had an insignificant effect on the calculated NEXAFS spectra, we used the same B3LYP functional for all optimizations and TDDFT calculations for consistency and reduced computational cost.